title: Next Generation Sequencing Facilitates Quantitative Analysis of  ApoE-/-/SAHHWT, ApoE-/-/SAHH+/- mice and ApoE-/-/SAHH+/- +Betaine mice [WGBS]

first: xin

last: dai

overall_design: Methods: Mouse vascular tissue methylation profiles of ApoE-/-/SAHHWT, ApoE-/-/SAHH+/- mice and ApoE-/-/SAHH+/- +Betaine mice were generated by deep sequencing, in triplicate. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated. Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.20.0).

first: Xin

last: Dai


title: Comparison of rare vs macroscopic human prostate cancer cells in mouse bone

status: Public on Oct 21 2021

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Luciferase and GFP labeled Du145 prostate cancer cells were injected into the left cardiac ventricle of CB17 SCID mice and allowed to grow until tumors were detectable in bones. FACS was used to isolate prostate cancer cells as described (Cackowski et al, J Cellular Biochemistry 2017) from bones with detectable tumor or the remaining pelvis, lumbar vertebrae, femorae, tibiae and humorae which had tumor cells present but below the limit of detection by imaging. After RNA isolation and cDNA synthesis, the samples were profiled by bulk RNA sequencing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Pairwise comparison of bones grossly involved with tumor vs. bones where tumor was not detected by imaging, from two mice.

first: Frank

last: Cackowski

first: Russel

middle: S

last: Taichman

first: Laura

last: Buttitta


title: Transcriptional changes over time in exploring cultures of Streptomyces venezuelae [three growth timepoints]

status: Public on Oct 22 2021

city: Hamilton

first: Evan

last: Shepherdson

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

summary: We isolated and sequenced mRNA from Streptomyces venezuelae grown on solid medium that promotes exploratory behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time.

overall_design: Streptomyces venezuelae mRNA profiles isolated from exploring cultures at three growth timepoints; two replicates each. Changes in gene expression compared using DeSeq2

first: Marie

middle: A

last: Elliot

first: Yordan

last: Stoyanov


title: Maternal protein restriction changes skeletal muscle metabolism and structural gene expression in aging rats

city: Botucatu

first: Bruno

middle: Evaristo de Almeida

last: Fantinatti

state: São Paulo

address: Prof Antonio Celso Wagner Zanin

department: Morphology

country: Brazil

institute: Unesp

summary: We intended to evaluate the phenotypic characteristics of the muscle microenvironment, involving muscle fiber and extracellular matrix, in skeletal muscle of elderly rats, at 540 days, arising from maternal protein restriction.

overall_design:
Maternal protein restriction affects the postnatal skeletal muscle physiology with effects lasting until senility. Considering the different muscle adaptations after maternal protein restriction observed in previous studies, transcriptomic analysis has proven to be an excellent strategy to understand the impacts of fetal programming on skeletal muscle.
To investigate the morphological, metabolic, and molecular characteristics of skeletal muscle in aged rats subjected to maternal protein restriction, we used aged male rats (540 days old) born from dams fed with protein restricted diet (6% protein) during
gestation and lactation. Using molecular and morphological techniques, we evaluated the Soleus (SOL) and Extensor Digitorum Longus (EDL) muscles. Muscle fiber crosssectional area (CSA) was measured and gene expression of oxidative (Succinate Dehydrogenase-Sdha and Citrate Synthase-CS) and glycolytic (Lactate Dehydrogenase-Ldha) markers were evaluated by RT-qPCR. Global transcriptome analysis also was performed to identify deregulated genes, following the RT-qPCR validation. The oxidative SOL muscle displayed decrease in muscle fiber CSA and in the expression of oxidative metabolism marker, up-regulation of anabolic Igf-1, structural Chad, and Fmod gene, and down-regulated Hspb7 gene. The glycolytic EDL muscle had no changes in muscle fiber CSA and in expression of oxidative metabolism genes, while the gene expression of Chad was up-regulated and Myog
gene was down-regulated. Collectively, our data show that maternal protein restriction induced changes in the expression of metabolic, anabolic, myogenic and structural genes, mainly in oxidative SOL muscle, in aged offspring rats.

first: Jéssica

last: Valente

first: Érika

last: Perez

first: Bruna

middle: T

last: Zanella

first: Tassiana

middle: G

last: Paula

first: Sérgio

last: Santos

middle: O

last: Duran

first: Robson

middle: F

last: Carvalho

first: Luiz

last: Justulin

middle: E

first: Maeli

middle: D

last: Silva


title: Next Generation Sequencing Facilitates Quantitative Analysis of  ApoE-/-/SAHHWT, ApoE-/-/SAHH+/- mice and ApoE-/-/SAHH+/- +Betaine mice

city: shenzhen

first: xin

last: dai

address: 628 Zhenyuan Road

country: China

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Transcriptome of 84 garlic accessions

status: Public on Oct 20 2021

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: A total of 84 diverse germplasms collected from 13 countries were performed for population transcriptomic analysis. Then, Pearson’s correlation analysis was performed between four bulb traits and FPKM values of each gene in 84 accession, thereby to identify genes with an expressed association with bulb traits.

overall_design: Three enlarging-growth bulbs of each accessions were collected and performed for RNA sequencing.


title: Development and validation of an open-source, disposable, 3D-printed in vitro environmental exposure system for Transwell® culture inserts

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

department: Biology

institute: University of Waterloo

summary: Accessible in vitro models recapitulating the human airway that are amenable to study whole cannabis smoke exposure are needed for immunological and toxicological studies that inform public health policy and recreational cannabis use. In the present study, we developed and validated a novel 3D printed In Vitro Exposure System (IVES) that can be directly applied to study the effect of cannabis smoke exposure on primary human bronchial epithelial cells. Using commercially available design software and a 3D printer, we designed a four-chamber Transwell® insert holder for exposures to whole smoke. Software was used to model gas distribution, concentration gradients, velocity profile and shear stress within IVES. Following simulations, primary human bronchial epithelial cells cultured at air-liquid interface on Transwell® inserts were exposed to whole cannabis smoke. IVES represents an accessible, open-source, exposure system that can be used to model varying types of cannabis smoke exposures with human airway epithelial cells grown under air-liquid interface culture conditions.

overall_design: Paired primary human bronchial epithelial cells obtained from 5 patients were cultured at air-liquid interface on Transwell® inserts and exposed to whole cannabis smoke (N=5) or air (N=5). Following 24 hours, outcome measurements included cell morphology, epithelial barrier function, lactate dehydrogenase (LDH) levels, cytokine and gene expression. Whole smoke delivered through IVES possesses velocity profiles consistent with uniform gas distribution across the four chambers and complete mixing. Airflow velocity ranged between 1.0-1.5 μm s-1 and generated low shear stresses (<< 1 Pa). Human airway epithelial cells exposed to cannabis smoke using IVES showed changes in cell morphology and disruption of barrier function without significant cytotoxicity. Cannabis smoke elevated IL-1 family cytokines and elevated CYP1A1 and CYP1B1 expression relative to control.

first: Abiram

last: Chandiramohan

first: Mohammedhossein

last: Dabaghi

first: Nicholas

last: Tiessen

first: Mary

last: Stewart

first: Quynh

last: Cao

first: Jenny

middle: P

last: Nguyen

first: Nima

last: Makhdami

first: Gerard

last: Cox

first: Andrew

middle: C

last: Doxey

first: Jeremy

last: Hirota


title: Thermal transcriptome

city: Colchester

first: Liudmila

last: Mikheeva

address: Wivenhoe Park

country: United Kingdom

institute: University of Essex

sample_organism:
Synechocystis sp. PCC 6803
Phaeodactylum tricornutum


title: Thermal transcriptome of Phaeodactylum tricornutum in steady-state growth

summary: Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal acclimation in the model diatom species Phaeodactylum tricornutum by comparing the differential gene expression in cultures acclimated to sub-optimal, optimal, and supra-optimal temperatures (10, 20 and 26.5 °C, respectively).

overall_design: Cultures (n=4) of Phaeodactylum tricornutum were grown for more than 10 generations at three temperatures (10, 20 and 26.5 °C). Cells were harvested in exponential growth phase by filtering at least 50 mL on to a polycarbonate membrane and flash freezing in liquid nitrogen. Cultures grown at 20 °C are used as a reference transcriptome.

first: Richard

middle: J

last: Geider

first: Kirralee

last: Baker

first: Tracy

last: Lawson

first: Ulrike

last: Bechtold


title: TET1 knockdown cancer cell lines

city: Albuquerque

first: Steven

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

type: Methylation profiling by genome tiling array


title: Expression of CCRL2 inhibits tumor growth by concentrating chemerin and inhibiting neoangiogenesis

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: CCRL2 is a non-signaling G protein-coupled receptor for chemerin, a leukocyte chemoattractant and an adipokine. Graft of B16 melanoma or Lewis lung carcinoma (LLC) cell lines in CCRL2 KO mice results in delayed growth of the tumors.

overall_design: mRNA profiles of LLC and B16 tumors (5 days following graft in the back of syngeneic C57BL/6 mice) in CCRL2 WT or KO mice were generated, in duplicate, using Illumina Hiseq1500.

first: Diana

last: Delbany

first: Virginie

last: Robert

first: Ingrid

last: Dubois-Vedrenne

first: Annalisa

last: Del Prete

first: Maxime

last: Vernimmen

first: Ayoub

last: Radi

first: Anne

last: Lefort

first: Frédérick

first: Valérie

last: Wittamer

first: Silvano

last: Sozzani

first: Marc

last: Parmentier


title: Trav15-dv6 family Tcrd rearrangements diversify the Tcra repertoire

city: Durham

first: Danielle

last: Dauphars

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University

summary: Dauphars et al. show that prior Tcrd rearrangement is essential for a combinatorially diverse Tcra repertoire in mouse thymocytes. Trav15-dv6 family Tcrd rearrangements are critical for Tcra repertoire formation because of their central and distal locations in the Va-Vd array.

overall_design: High-throughput sequencing was used to analyze Tcra repertoire from RNA purified from sorted DP thymocytes from groups of 2 mice bearing either wild-type or genetically modified Tcra-Tcrd alleles.

first: Ariana

last: Mihai

first: Liuyang

last: Wang

first: Yuan

last: Zhuang

first: Michael

last: Krangel


title: Transcriptomic profiling of adult-onset asthma related to damp and moldy buildings and idiopathic environmental intolerance [blood]

city: Helsinki

first: Piia

last: Karisola

state: Southern Finland

address: Haartmaninkatu 3

department: Medical Faculty, Human Microbes Research Program Unit

country: Finland

institute: University of Helsinki

summary: The objective of the study was to characterize distinct endotypes of asthma related to damp and moldy buildings and to evaluate the potential molecular similarities with idiopathic environmental intolerance (IEI). The blood cell transcriptome of 88 study subjects was profiled using peripheral blood mononuclear cell (PBMC) samples obtained at baseline.

overall_design: Venous blood samples were collected from female adult-onset asthma patients (n=50), IEI patients (n=17) and healthy subjects (n=21) yielding 88 study subjects. PBMCs were separated and total RNA extracted for microarray analyses.

first: Hille

last: Suojalehto

first: Joseph

last: Ndika

first: Irmeli

last: Lindström

first: Liisa

last: Airaksinen

first: Paula

last: Kauppi

first: Kirsi

last: Karvala

first: Antti

last: Lauerma

first: Sanna

middle: K

last: Toppila-Salmi

first: Harri

last: Alenius


title: Transcriptomic profiling of adult-onset asthma related to damp and moldy buildings and idiopathic environmental intolerance [nasal biopsy]

summary: The objective of the study was to characterize distinct endotypes of asthma related to damp and moldy buildings and to evaluate the potential molecular similarities with idiopathic environmental intolerance (IEI). The nasal biopsy transcriptome of 88 study subjects was profiled using samples obtained at baseline.

overall_design: Nasal biopsy samples were collected from female adult-onset asthma patients (n=45), IEI patients (n=14) and healthy subjects (n=21) yielding 80 study subjects. Biopsies were homogenized and total RNA extracted for microarray analyses.


title: Next Generation Sequencing was performed on MDSCs from tumors of control or alisertib treated tumor-bearing mice

city: Hefei

first: tingting

last: Yin

address: Daoxiang Village

institute: University of Science and Technology of China

summary: The Aurora-A inhibitor alisertib shows encouraging activities in clinical trials against multiple malignances including advanced breast cancer. However, its mechanism of action remains unclear, especially regarding how the inflammatory microenvironment is involved in the efficacy of alisertib. Here, we demonstrated that Aurora-A inhibition directly reshapes the immune microenvironment through removal of tumor-promoting myeloid cells and enrichment of anti-cancer T lymphocytes, which restores a tumor-suppressive microenvironment and significantly contributes to the regression of murine mammary tumors. Mechanistically, the Aurora-A inhibitor effectively eliminated myeloid cells including myeloid-derived suppressor cells (MDSCs) and macrophages in tumors by triggering apoptosis of these cells. Further, Aurora-A inhibition could disrupt the immunosuppressive functions of MDSCs through inhibiting Stat3 mediated ROS production. These alterations led to significant increases in the proportion and the number of CD8+ and CD4+ T lymphocytes, which efficiently inhibited the proliferation of tumor cells. In summary, these data revealed that in addition to suppressing the proliferation of tumor cells, Aurora-A inhibitor directly modulates and restores an anti-tumor immune-microenvironment in breast cancer. Intriguingly, Aurora-A inactivation combined with PD-L1 blockade showed synergistic efficacy in the treatment of mammary tumors, providing an effective strategy for clinical trials of chemo-immunotherapy in breast cancer.

overall_design: TA-MDSCs were sorted from 20 tumors of  alisertib treated tumor bearing mice and pooled together. TC-MDSCs were sorted from 20 tumors of  control  tumor bearing mice and pooled together. BM-neu were sorted from the bone marrows of 5 WT BALB/c mice.

first: Tingting

first: Zhi-Bin

last: Zhao


title: Next Generation Sequencing of CD8+ and CD4+ cells isolated from angiotensin-2 treated mice

city: Pozzilli

first: Daniela

last: Carnevale

address: Via dell'Elettronica

country: Italy

institute: IRCCS Neuromed and "Sapienza" University of Rome

summary: RNA-sequencing of CD8 lymphocytes isolated from pre-hypertensive mice revealed upregulation of gene pathways involved in MAPK cascade, positive regulation of intracellular calcium fluxes, response to IFN-g and other external stimuli, and lymphocyte chemotaxis, as compared to CD4 T cells. Taken together these results indicate that hypertensive stimuli program CD8 T cells toward a phenotype with pro-migratory properties that might account for their ability to enhance myogenic  tone of resistance arteries

overall_design: RNA sequencing of FACS-sorted CD4+ and CD8+ cells from Angiotensin-2 treated mice

first: Lorenzo

first: Sara

last: Perrotta

first: Fabio

last: Pallante

first: Agnese

last: Migliaccio

first: Marialuisa

first: Daniele

last: Iodice

first: Giuseppe

last: Lembo


title: MKK4/5-MPK3/6 cascade regulates Agrobacterium-mediated transformation by modulating plant immunity in Arabidopsis

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

summary: Agrobacterium tumefaciens is a special plant pathogen causing crown gall disease. This pathogen is well known for the technology Agrobacterium-mediated transformation. As a pathogen, Agrobacterium triggers plant immunity, and this affects transformation. But the signaling components and pathways in plant immunity to Agrobacterium remain elusive.     We demonstrate two Arabidopsis MAPKKs MKK4/MKK5 and their downstream MAPKs MPK3/MPK6 play a major role in both Agrobacterium-triggered immunity and Agrobacterium-mediated transformation. Agrobacteria induce MPK3/MPK6 activity and plant defense responsive genes expression in a very early stage. This process is dependent on MKK4/MKK5 function.     Loss of function of MKK4 and MKK5 or their downstream MPK3 and MPK6 abolishes plant immunity to agrobacteria, and increases the transformation frequency, while activation of MKK4 and MKK5 enhances the plant immunity and represses the transformation. Global transcriptome indicates agrobacteria induce various plant defense pathways, including ROS production, ethylene and SA-mediated defense responses, and MKK4/MKK5 is essential for these pathways induction. Activation of MKK4 and MKK5 promotes ROS production and cell death in agrobacteria infection process. Ethylene and SA act bypass of MKK4/MKK5 signaling to regulate transformation.    Based on these results, we propose MKK4/5-MPK3/6 cascade is an essential signaling pathway to regulate Agrobacterium-mediated transformation by modulating Agrobacterium-triggered plant immunity.

overall_design: RNA-seq profile of WT and mkk4/5 double mutant after agrobacteria infection

first: Kaixuan

last: Duan

first: Tengfei

last: Liu


title: BulkRNAseq - Neurotransmitters regulate distinct phases of multimodal human interneuron migration

city: Vienna

first: Sunanjay

last: Bajaj

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Institute for Molecular Biotechnology of the Austrian Academy of Sciences

summary: We use cerebral organoid fusions and a novel migration tracking platform to understand the functional impact of neurotransmitter signaling on migrating human interneurons.

overall_design: Seven unique groups: (I) GFP- cells – single dorsal organoids (II) GFP+ cells – single ventral organoids (III) GFP- cells – single ventral organoids (IV) GFP+ cells – dissected ventral regions of fusions (V) GFP- cells – dissected ventral regions of fusions (VI) GFP+ cells – dissected dorsal regions of fusions (VII) GFP- cells – dissected dorsal regions of fusions. In total, 32 single organoids and 34 fusions were used to obtain 52 samples for the RNA sequencing analysis.

first: Joshua

last: Bagley

first: Christoph

last: Sommer

first: Abel

last: Vertesy

first: Veronica

last: Krenn

first: Sakurako

last: Wong

first: Julie

last: Lévi-Strauss

first: Juergen

last: Knoblich


title: IAPP-induced beta cell toxicity recapitulates islet molecular pathology in type 2 diabetes

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Islets in Type 2 diabetes (T2D) share many diverse abnormalities reported in neurodegenerative diseases, including the formation of toxic oligomers from amyloidogenic proteins. We evaluated the transcriptome of murine islets with beta cell-specific human IAPP (hIAPP) expression to assess the potential contribution of hIAPP toxicity to those observed in islets from T2D.Beta cell hIAPPtoxicity induced an islet transcriptome highly analogous to that in islets from humans with T2D with a prominent inflammatory signature, activation of vascular epithelium and stellate cells, cytoskeleton remodeling,and activation of cell-cycle andcellular dedifferentiation. In conclusion, many of the apparently widely disparate changes in islets in T2D may be initiated by toxic oligomers. Inhibition of expression of amyloidogenic proteins or proximal adverse consequences such as disruption of the cytoskeleton by calpain hyperactivation are rational targets for therapeutic intervention in T2D and neurodegenerative disease.

overall_design:
RNA-seq of bulk pancreatic islets from 9-10 week old hIAPP, rIAPP, hIAPP:hCAST, hCAST and WT mice (15 samples; n = 3 per group)

Treatment descriptions:
hIAPP: Transgenic expression of human IAPP under insulin II promoter
hIAPP_hCAST: Transgenic expression of human IAPP under insulin II promoter; transgenic expression of human CAST under insulin
rIAPP: Transgenic expression of rodent IAPP under insulin II promoter
hCAST: Transgenic expression of human CAST under insulin II promoter

first: Allison

last: Furterer

first: Tatyana

last: Gurlo

first: Qing

last: Wang

first: Fuying

last: Gao

first: Madeline

last: Rosenberger

first: Lina

last: Pei

first: Hiroshi

last: Nomoto

first: Alex

middle: M

last: Mawla

first: Mark

last: Huising

first: Giovanni

last: Coppola

first: Peter

last: Butler


title: Multiomic study of skin/peripheral blood cell transcriptome and serum proteins: Is serum proteome a reflection of disease process at the end-organ level in systemic sclerosis?

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 Fannin

department: Division of Rheumatology

institute: The University of Texas Health Science Center at Houston

summary: This is a global gene expression study of peripheral blood cell samples collected from a subset of 49 systemic sclerosis patients enrolled in the GENISOS cohort, as well as unaffected controls.

overall_design: Peripheral blood cell samples from 49 patient enrolled in the GENISOS cohort and 25 controls were examined by global gene expression studies. The associated skin samples are uploaded under GSE58095 with matching sample ID labels.

first: Victor

last: Farutin

first: Elma

last: Kurtagic

first: Joel

middle: R

last: Pradines

first: Ishan

last: Capila

first: Maureen

last: Mayes

first: Minghua

last: Wu

first: Anthony

last: Manning


title: Transcriptomic profiling of adult-onset asthma related to damp and moldy buildings and idiopathic environmental intolerance

first: Piia

last: Karisola


title: Thermal transcriptome of Synechocystis in response to gradual heat stress

first: Liudmila

last: Mikheeva

summary: Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal stress in the model cyanobacteria species Synechocystis. We impose gradual heat stress by increasing the temperature in a stepwise fashion (1.5 °C h-1) from their optimal growth temperature of 30 °C to a maximum temperature of 46.5 °C over a period of 12h.

overall_design: Cultures (n=6) of Synechocystis were grown for more than 10 generations at optimal temperature conditions of 30 °C using continuous culture methods. Three cultures were exposed to the gradual heat stress (Treatment), whilst the other three cultures were maintained under stock culture conditions (Control). All cultures were sampled every hour creating a time series of 12 equally spaced time points.  Cells were harvested by filtering at least 50 mL on to a polycarbonate membrane and flash freezing in liquid nitrogen.

first: Richard

last: Geider

first: Kirralee

last: Baker

first: Tracy

last: Lawson

first: Ulrike

last: Bechtold


title: Nucleolin aptamer N6L reprograms the translational machinery and acts synergistically with mTORi to inhibit pancreatic cancer proliferation

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: We previously showed that N6L, a pseudo-peptide that targets nucleolin, impairs pancreatic ductal adenocarcinoma (PDAC) growth and normalizes tumor vessels in animal models. In this study, we analyzed the translatome of PDAC cells treated with N6L to identify the pathways that were either repressed or activated. We observed a strong decrease of global protein synthesis. However, about 6% of the mRNAs were enriched in the polysomes. We identified a 5’TOP motif in many of these mRNAs, and demonstrated that a chimeric RNA bearing a 5‘TOP motif was up-regulated by N6L. We demonstrated that N6L activates the mTOR pathway which is required for the translation of these mRNAs. An inhibitory synergistic effect in PDAC cell lines including patient derived-xenografts and tumor derived-organoids was observed when N6L was combined with mTOR inhibitors. In conclusion, N6L reduces pancreatic cells proliferation which then undergoes a translational reprogramming through activation of the mTOR pathway. N6L and mTOR inhibitors act synergistically to inhibit the proliferation of PDAC and human PDX cell lines. This combotherapy of N6L and mTOR inhibitors could constitute a promising alternative to treat pancreatic cancer.

overall_design: Transcriptome of PDAC cell comparments (polysom and cytoplam) treated with nucleolin inhibitor vs control

first: Mounira

last: Chalabi-Dchar

first: Elisabeth

last: Cruz

first: Hichem

last: Mertani

first: Jean-Jacques

last: Diaz

first: José

last: Courty

first: Ilaria

last: Cascone

first: Fanny

last: Coulpier

first: Laurent

last: Jourdren

first: Philippe

last: Bouvet


title: scRNA-seq of atherosclerotic plaques of Apoe-/- mouse (with or without specific SMC KO of Has3)

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

summary: NOT PROVIDED; REQUESTED

first: Felicia

last: Harmann


title: Chromatin accessibility changes in experimentally-induced basal to squamous cell carcinoma transition (BST) upon EGFR/MAPK inhibitor treatments [ASZ_ATACseq_inhibitor]

city: Stanford

first: Anthony

last: Oro

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that modulation of Ras/MAPK or TGFb signaling drive BST. Here, we induce Ras/MAPK and/or abrogate TGFb signaling to induce BST. Alternatively we drive c-FOS to induce BST. Here, we analyze chromatin accessibility profiles upon c-FOS activation

overall_design: Methods: ATACseq profiles of ASZ transfected with doxycycline-inducible empty vector (ctrl) and c-FOS containing vector (c-FOS) upon Dox treatment with or without EGFR/MAPK inhibitor treatments, were generated by deep sequencing, in duplicate, using Illumina NovaSeq. The sequence reads that passed quality filters were analyzed using bowtie for alignment and macs2 for peak calling

first: Nancy

last: Li

first: Sadhana

last: Gaddam


title: The Adeno-Associated Virus 2 (AAV2) genome and Rep 68/78 proteins interact with cellular sites of DNA damage.

city: Madison

first: Kinjal

last: Majumder

state: WI

address: 1525 Linden Drive

department: Oncology

institute: University of Wisconsin

summary: We have previously developed a modified iteration of a viral chromosome conformation capture (V3C-seq) assay to show that the autonomous parvovirus Minute Virus of Mice (MVM) localizes spatially with cellular sites of DNA damage to establish viral replication centers. Similar V3C-seq assays to map AAV genome localization show that both replicating and non-replicating AAV2 genomes in the absence of helper virus colocalize with cellular sites of DNA damage. The AAV non-structural protein Rep 68/78, when ectopically expressed in the absence of viral infection or during AAV2 infection in the absence of helper proteins also localizes to cellular sites of DNA damage. Strikingly however, recombinant AAV gene therapy vector genomes derived from AAV do not colocalize with AAV and Rep at cellular DDR sites.

overall_design: Identification of cellular interaction site of the dependoparvovirus AAV2, and the localization of the resultant DNA damage response. Independent replicates of chromosome conformation capture (designated as V3C in the file name) and ChIP-seq experiments (the target epitope provided in the name) have been performed. For each time-point or treatment, at least two independent replicates of the indicated assays have been performed. ChIP-seq assays have been normalized to total input DNA prior to rpm normalization. Chromosome conformation capture assays have been rpm normalized. A total number of 96 samples have been deposited. "hpd" designates hours post induction with doxycycline, and "hpi" designates hours post infection with the dependoparvovirus Adeno-associated Virus 2 or with recombinand AAV (rAAV).

first: Maria

last: Boftsi

first: David

last: Pintel


title: Thermal transcriptome of Phaeodactylum tricornutum in response to gradual heat stress

first: Liudmila

last: Mikheeva

summary: Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal stress in the model diatom species Phaeodactylum tricornutum. We expose cultures to high temperature (optimal +8°C) and follow changes in gene expression through time (over a 12 hour period) in comparison to optimal conditions  (20 °C).

overall_design: Cultures (n=4) of Phaeodactylum tricornutum were grown for more than 10 generations at optimal temperature conditions of 20 °C. Each culture was split to form a Control (maintained at 20 °C) and Treatment (subjected to 28 °C ). Both the control and treatments were sampled every hour creating a time series of 12 equally spaced time points.  Cells were harvested by filtering at least 50 mL on to a polycarbonate membrane and flash freezing in liquid nitrogen.

first: Richard

last: Geider

first: Kirralee

last: Baker

first: Tracy

last: Lawson

first: Ulrike

last: Bechtold


title: NanoString analysis of gene expression by compound 2D216 and/or LPS in mouse bone marrow-derived dendritic cells (BMDC)

city: La Jolla

first: Tomoko

last: Hayashi

state: California

address: 9500 GIlman Drive

institute: UC San Diego

summary: Mouse BMDCs were treated with vaccine adjuvant candidate compound 2D216 and/or LPS and differential gene expression was analyzed by NanoString to examine mode of action of compound 2D216

overall_design: Differentially expresed gene analysis by NanoString


title: Enhanced susceptibility of ADAP-deficient mice to Listeria monocytogenes infection is associated with an altered phagocyte phenotype and function

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

summary: The adhesion and degranulation-promoting adaptor protein (ADAP) serves as a multifunctional scaffold and is involved in the formation of immune signaling complexes. To date only limited data exist regarding the role of ADAP in pathogen-specific immunity during in vivo infection and its contribution in phagocyte-mediated antibacterial immunity remains elusive. Here we show that mice lacking ADAP (ADAPko) are highly susceptible to the infection with the intracellular pathogen Listeria monocytogenes (Lm) by showing enhanced immunopathology in infected tissues together with increased morbidity, mortality and excessive infiltration of neutrophils and inflammatory monocytes. Despite high phagocyte numbers in spleen and liver, ADAPko mice only inefficiently controlled pathogen growth hinting at a functional impairment of infection-primed phagocytes in the ADAP-deficient host. Flow cytometric analysis of hallmark pro-inflammatory mediators and unbiased whole genome transcriptional profiling of neutrophils and inflammatory monocytes uncovered broad molecular alterations in the inflammatory program in both phagocyte subsets following their activation in the ADAP-deficient host. Strikingly, ex vivo phagocytosis assay revealed impaired phagocytic capacity of neutrophils, and, inflammatory monocytes derived from Lm-infected ADAPko mice. Together, our data suggest that an alternative priming of phagocytes in ADAP-deficient mice during Lm infection induces marked alterations in the inflammatory profile of neutrophils and inflammatory monocytes that contribute to enhanced immunopathology while limiting their capacity to eliminate the pathogen and to prevent the fatal outcome of the infection.

overall_design: In total 23 microarrays were analysed. Neutrophils and inflammatory monocytes were FACS-sorted from spleen and liver leukocytes from Lm-infected wild type and ADAPko mice 3 days post infection. Mice were on C57BL/6 genetic background. RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. To acquire a representative mix of all individual samples (n = 6 mice/genotype), sorted cells from two mice per genotype were pooled. Each genotype was analyzed in triplicates. Only neutrophils from wild type mice were analyzed in duplicate.

first: Martha AL

last: Böning

first: Gerald

last: Parzmair

first: Henning

last: Düsedau

first: Olivia

last: Kershaw

first: Baolin

last: Xu

first: Borna

last: Relja

first: Dirk

last: Schlüter

first: Ildiko

last: Dunay

first: Annegret

last: Reinhold

first: Burkhart

last: Schraven

first: Dunja

last: Bruder


title: Effect of chronic low dose of cadmium chloride exposure on long non-coding RNA expression in human bronchial epithelial BEAS-2B cells

city: Cleveland

first: Chengfeng

last: Yang

state: OHIO

address: 2500 MetroHealth Drive

department: Medicine

institute: Case Western Reserve University

summary: BEAS-2B cells were continuously exposed to 2.5 uM of cadmium chloride for 9 months and the expresssion of lncRNAs were analyzed by lncRNA microarray analysis.

overall_design: Total RNAs were extracetd from passage-matcehd control BEAS-2B cells and cdmium-exposed BEAS-2B cells and submitted for lncRNA microarray analysis


title: Comparative transcriptome of proliferative cells, dormant cells and awaken cells throught a DDR1 depletion

city: New York

first: Jose Javier

last: Bravo Cordero

state: NY

address: 1468 Madison Avenue, Annenberg 24-34

institute: Icahn School of Medicine at Mount Sinai

summary: The goal of this study is to compare the trancriptome of proliferative THEP3 cells to their dormant counterpart DHEP3 and an awaken version through DDR1 receptor depletion (shRNA control verus shRNA DDR1) to identify target genes involved in the dormancy state and the awakening process from where metatsiss will arise.

overall_design: cells were injected in nude mice and grown for 2 weeks. Then tumors were collected and total RNA were extracted and shipped to Novogene Co., Ltd in Sacramento CA, USA for library construction, sequencing and data processing.

first: Julie

last: Di Martino

first: Elana

last: Fertig

first: Jose

last: Bravo-Cordero


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and MttpIKO liver Transcriptomes on methioine defcient diet (MCD)

city: St. Louis

first: Yan

last: Xie

state: MO

address: 660 South Euclid

department: Gastroenterology

institute: Washington University School of Medicine in St louis

summary: Purpose: The goals of this study is to use NGS-derived liver transcriptome profiling (RNA-seq) to identify candidates of pathways and genes which are responsible to protect MttpIKO from MCD induced-NASH development  .

overall_design: Mttpf/fVillin Cre mice were injected with Tamoxifen or vehicle and Keep on MCD diet for 3 weeks. Livers were collected after 4 hours fasting. Total liver RNA were extracted by TriZol reagent and 3 RNA pools (from 12 liver  RNA) by genotype were submited for NGS.

first: Nicholas

last: Davidson


title: Human amniotic epithelial stem cell-derived retinal pigment  epithelium cells repair retinal degeneration

city: Hangzhou

first: jin

middle: ying

last: li

state: -- Select State/Province --

address: No. 866 Yuhangtang Road

institute: Zhejiang University

summary: Age-related macular degeneration (AMD), featured with dysfunction and loss of retinal pigment epithelium (RPE), is lacking efficient therapeutic approaches. According to our previous studies, human amniotic epithelial stem cells (hAESCs) may serve as a potential seed cell source of RPE cells for therapy because they have no ethical concerns, no tumorigenicity, and little immunogenicity. Herein, trichostatin A and nicotinamide can direct hAESCs differentiation into RPE like cells. The differentiated cells display the morphology, marker expression and cellular function of the native RPE cells, and noticeably express little MHC class II antigens and high level of HLA-G. Importantly, visual function and retinal structure of Royal College of Surgeon (RCS) rats, a classical animal model of retinal degeneration, were rescued after subretinal transplantation with the hAESCs-derived RPE like cells. We established a high-efficient, low-cost and safety-guaranteed system for generating functional RPE cells from hAESCs. These results suggest a novel and ideal therapeutic strategy for retinal degeneration diseases

overall_design: we showed the mRNA expression pattern between hAESCs-RPE cells and hfRPE cells

first: Jinying

last: Li

first: Chen

last: Qiu


title: Discovering Myeloid Cell Heterogeneity in Alveolar Bone –Cell by Cell Analysis

city: Buffalo

first: Jonathan

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

summary: Site-specific differences in the myeloid progenitor cellular composition and transcriptional programs providing a deeper appreciationof the complex differences in myeloid cell heterogeneity from different anatomical bone marrow sites.

overall_design: 10x scRNA-Seq of Mandible and Femur bone marrow populations

first: Keith

last: Kirkwood

first: Kyu

middle: H

last: Kwack

first: Natalie

last: Lamb

first: Elliot

last: Kramer

first: Lixia

last: Zhang

first: Scott

middle: I

last: Abrams

middle: L


title: Transcriptional changes in experimentally-induced basal to squamous cell carcinoma transition (BST) upon treatment with small molecule inhibitors [ASZ_RNAseq_inhibitor]

first: Anthony

last: Oro

summary: Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that either modulation of Ras/MAPK or TGFb signaling or c-FOS induction could drive BST. Enhanced EGFR signaling has been implicated during BST. Here, we analyze transcriptional profiles upon c-FOS induction when cells are treated with EGFR signaling inhibitors afatinib (5uM) and UO126 (10uM).

overall_design: Methods: mRNA profiles of ASZ transfected with doxycycline-inducible empty vector (ctrl) or c-FOS containing vector (c-FOS) upon Dox treatment (24h) followed by EGFR signaling inhibitor treatments (6h) or DMSO control, were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Homer.

first: Nancy

middle: Y

first: Sadhana

last: Gaddam


title: Characterization of the immune response in patients with cancer of the oral cavity after neoadjuvant immunotherapy with the IRX-2 regimen

city: Ann Arbor

first: Siyu

last: Liu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

summary: IRX-2 is a homologous cell-derived multi-cytokine biologic with multifaceted immune modulatory effects that has been shown to induce increased lymphocyte infiltration into primary tumors in oral cavity carcinoma. Our objective was to characterize tumor immune gene expression and epigenomic changes after neoadjuvant IRX-2 immunotherapy in patients with squamous cell carcinoma of the oral cavity.

overall_design:
A randomized phase II trial was conducted of the IRX regimen 3 weeks prior to surgery. The treatment regimen consisted of cyclophosphamide (day 1) followed by 10 days of regional perilymphatic IRX-2 cytokine injections and daily oral indomethacin, zinc and omeprazole (Regimen 1) compared to the identical regimen without the IRX-2 cytokines (Regimen 2). NanoString immune panel (730 genes) and Infinium MethylationEPIC BeadChip were performed to assess the gene expression and DNA methylation signatures, respectively in pre- and post-treatment tumor samples.
contributor: INSPIRE Trial Clinical Investigators

first: Emily

last: Bellile

first: Ariane

last: Nguyen

first: Katie

last: Zarins

first: Laura

last: Rozek

first: Gregory

last: Wolf

first: Maureen

last: Sartor


title: Heading towards a dead end: the role of DND1 in germ line differentiation of human iPSCs

city: Muenster

first: Stefan

last: Schlatt

state: NRW

address: Albert-Schweitzer Campus 1, Building D11

department: Centre of Reproductive Medicine and Andrology

institute: Muenster University Hospital

summary: We knocked out DND1 in human iPSCs and analysed its role in pluripotency and differentiation. We showed that general pluripotency gene expression is not affected, but KO iPSCs differentiate less efficiently towards PGC-like cells and remaining PGCLCs show reduced expression of NANOS3 and PRDM1.

overall_design: We examine the effects of DND1 KO during human germ cell differentiation. Experiments were performed in iPSC, iMeLCs and PGCLC. For each cell type there is one Wild Type (WT) sample and three DND1 Knock Outs (KO). Each set of samples is run in duplicates.

first: Eva

last: Mall

first: Aaron

last: Lecanda

first: Hannes

last: Drexler

first: Erez

last: Raz

first: Hans

last: Schöler


title: Tryptophan plays a central role in yeast’s tolerance to isobutanol

city: Taipei

first: Hsien-Lin

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

summary: Isobutanol is considered a potential biofuel and can be produced by genetically modified microorganisms. Saccharomyces cerevisiae inherently produces isobutanol through valine intermediate(s), so it serves as a good host. However, isobutanol's toxicity remains a key obstacle for bioproduction. In our study, we first used image recognition to screen the colony growth of a yeast gene deletion library and inferred that genes involved in tryptophan biosynthesis, ubiquitination, and the pentose phosphate pathway (PPP) contribute to isobutanol tolerance. The importance of tryptophan in yeast's tolerance to isobutanol was confirmed by the recovery of isobutanol tolerance in a tryptophan biosynthesis defective strain by adding exogenous tryptophan. Transcriptomic analysis revealed that amino acid biosynthesis- and transportation-related genes in a tryptophan biosynthesis defective host were up regulated under conditions such as nitrogen starvation. This may explain why ubiquitination for protein degradation was involved for the protein turnover. PPP metabolites and vitamin B1/B6 may serve as precursors and cofactors in tryptophan biosynthesis to enhance isobutanol tolerance. Furthermore, the tolerance mechanism may also be linked to tryptophan metabolism, including the kynurenine pathway and nicotinamide adenine dinucleotide biosynthesis. Both pathways are responsible for cellular redox balance and antioxidative ability and figured out that tryptophan may play a crucial role on isobutanol tolerance. Our study highlights the central role of tryptophan in yeast's isobutanol tolerance and offers new clues for engineering a yeast host with strong isobutanol tolerance.

overall_design: Wild type (WT) and tryptophan synthase (TRP5) defected strain Sc12 was cultured with/without isobutanol and/or tryptophan for 24 hours (n=3).

first: Wen

last: Li

first: Chieh

last: Huang

first: Hsien


title: SLCO1B3 promotes the progression of colorectal cancer cells by regulating the STAT3 pathway

city: shijiazhuang

first: liang

middle: hui

last: zhi

state: hebei

address: zhongshanxilu

institute: Bethune International Peace Hospital

summary:
Purpose: The purpose of this study was to analyze changes in the cell genome along with the downregulation of SLCO1B3, as well as changes in gene enrichment pathways, so as to find the downstream target genes of SLCO1B3
Conclusions: Our study is the first detailed analysis of SLCO1B3's effect on the genome of CRC cells.We concluded that changes in SLCO1B3 gene levels can lead to activation of multiple tumor-related signaling pathways, and that NGS provides a more comprehensive and accurate method for quantitative and qualitative assessment of cell mRNA content.

overall_design: HCT116 was transfected with the short interfering RNA (siRNA) specific for SLCO1B3 or negative control

first: Lianghui

last: Zhi

first: Guiying

last: Wang


title: ChIP-seq analysis of ENL following KAT6A CRISPR targeting

first: Jinyang

address: 1230 York Ave

institute: The Rockefeller University

summary: ChIP-seq analysis of ENL in MOLM-13 human leukemia cells transduced with lentivirus containing CRISPR-Cas9 EV or sgKAT6A for 5 days

overall_design: KAT6A promotes AML differentiation block. To test the effect of KAT6A inhibition on the genomic localization of ENL in AML cells, we utilized CRISPR-Cas9 technique and delete KAT6A in MOLM-13 human AML cells and performed ChIP-seq.

first: Fangxue

last: Yan

first: Andres

last: Blanco


title: Mechanisms of interindividual epigenetic variability at CpG dense transposable elements

city: Cambridge

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

institute: Univerity of Cambridge

summary: Profiling of DNA methylation and CxxC recruitment in Tc1 mice

overall_design: Refer to individual Series

first: Amy

last: Leung

first: Candi

last: Trac

first: Micheal

last: Lee

first: Mudasar

last: Basam

first: Dustin

last: Schones


title: Identification of distinct synovial fibroblast subsets associated with pain and progression of knee osteoarthritis using single-cell RNA sequencing

city: Bath

first: Amel

last: Badoume

address: Claverton Down

department: Pharmacy and Pharamcology

institute: University of Bath

summary: Synovial inflammation is associated with pain severity in patients with knee osteoarthritis (OA). The aim here was to determine in a population with knee OA, whether synovial tissue from areas associated with pain exhibited different synovial fibroblast subsets, compared to synovial tissue from sites not associated with pain. A further aim was to compare differences between early and end-stage disease synovial fibroblast subsets.   Parapatellar synovitis was significantly associated with the pattern of patient-reported pain in knee OA patients. Synovial tissue from sites of patient-reported pain exhibited a differential transcriptomic phenotype, with distinct synovial fibroblast subsets in early OA and end-stage OA. Functional pathway analysis revealed that synovial tissue and fibroblast subsets from painful sites promoted fibrosis, inflammation and the growth and activity of neurons. The secretome of fibroblasts from early OA painful sites induced neurite outgrowth in dorsal root ganglion neurons.  Sites of patient-reported pain in knee OA is associated with a different synovial tissue phenotype and distinct synovial fibroblast subsets. Further interrogation of these fibroblast pathotypes will increase our understanding of the role of synovitis in OA joint pain and provide a rationale for the therapeutic targeting of fibroblast subsets to alleviate pain in patients.

overall_design: Patients with early knee OA (n=29) and end-stage knee OA (n=22) were recruited. Patient reported pain was recorded by questionnaire and using an anatomical knee pain map. Proton density fat suppressed MRI axial and sagittal sequences were analysed and scored for synovitis. Synovial tissue was obtained from the medial and lateral parapatellar and suprapatellar sites. Fibroblast single cell RNA sequencing was performed using Chromium 10X and analysed using Seurat. Transcriptomes were functionally characterised using Ingenuity Pathway Analysis and the effect of fibroblast secretome on neuronal growth assessed using rat DRG.

first: Dominika

last: Nanus

first: Susanne

middle: N

last: Wijesinghe

first: Andrea

last: Halsey

first: Patrick

last: Hurley

first: Zubair

last: Ahmed

first: Rajesh

last: Botchu

first: Edward

middle: T

last: Davis

first: Mark

middle: A

last: Lindsay

first: Simon

middle: W

last: Jones


title: Identification of synovial fibroblasts subsets associated with pain and progression of knee osteoarthritis

city: Birmingham

address: Mindelsohn Way

department: Institute of Inflammation and Ageing

institute: University of Birmingham

summary:
Background: Synovial inflammation is associated with pain severity in patients with knee osteoarthritis (OA). The aim here was to determine in a population with knee OA, whether synovial tissue from areas associated with pain exhibited different synovial fibroblast transcriptomes, compared to synovial tissue from sites not associated with pain. A further aim was to compare differences between early and end-stage disease synovial fibroblasts.
Methods: Patients with early knee OA (n=29) and end-stage knee OA (n=22) were recruited. Patient reported pain was recorded by questionnaire and using an anatomical knee pain map. Proton density fat suppressed MRI axial and sagittal sequences were analysed and scored for synovitis. Synovial tissue was obtained from the medial and lateral parapatellar and suprapatellar sites. RNA sequencing was performed using Illumina’s NextSeq 500 and analysed with Galaxy web platform, usegalaxy.org, and Qlucore software. Transcriptomes were functionally characterised using Ingenuity Pathway Analysis.
Findings: Parapatellar synovitis was significantly associated with increased OA pain perception. Functional pathway analysis revealed that early OA painful sites mediate immune cell recruitment and promote the formation and development of neurites.
Conclusion: OA disease progression and the presence of pain in early OA is associated with different synovial pathotypes. Further interrogation of these pathotypes will increase our understanding of the role of synovitis in OA joint pain and provide a rationale for the therapeutic targeting to alleviate pain in patients.

overall_design: Transcriptomic profiling of early and end-stage knee OA synovium tissue from painful and non-painful sites.

middle: E

first: Archana

last: Sharma-Oates


title: Transcriptional changes in experimentally-induced basal to squamous cell carcinoma transition (BST) [ASZ_RasV12_TGFbR1_RNAseq]

first: Anthony

last: Oro

address: 269 Campus Drvie

institute: Stanford University

summary: Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that modulation of Ras/MAPK or TGFb signaling drive BST. Here, we induce Ras/MAPK and/or abrogate TGFb signaling to induce BST. Alternatively we drive c-FOS to induce BST. Here, we analyze transcriptional profiles upon Ras/MAPK activation and/or TGFb signaling abrogation.

overall_design: Methods: mRNA profiles of ASZ transfected with non-silencing (NS) or TGFbR1-targeting shRNA (TGFbR1kd) upon DMSO or Dox/4OHT treatment, were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Homer.

first: Francois

last: Kuonen

first: Sadhana

last: Gaddam


title: DNA binding profile of c-FOS in experimentally-induced basal to squamous cell carcinoma transition (BST)

summary: Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that modulation of Ras/MAPK or TGFb signaling drive BST. Here, we induce Ras/MAPK and/or abrogate TGFb signaling to induce BST and examine the DNA binding profile of the AP-1 transcription factor c-FOS.

overall_design: Methods: c-FOS ChIP binding profiles of ASZ transfected with TGFbR1-targeting shRNA (TGFbR1kd) upon Dox/4OHT treatment, were generated by deep sequencing, in duplicate, using Illumina NextSeq 500. The sequence reads that passed quality filters were analyzed using bowtie2 for alignment and macs2 for peak calling.

first: Nancy

last: Li


title: FFPE-samples from cavitational ultrasonic surgical aspirates are suitable for RNA profiling of gliomas

city: Alicante

first: Luis

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

summary: During surgical procedures of gliomas, tissular material obtained from cavitational ultrasonic surgical aspirators (CUSAs) is generally discarded but can exceed amount and quality of certain tumour core resections (TCRs). From archived FFPE-samples, we compared the profiles of somatic mutations and gene expression in the solid material from aspirates and TCRs obtained from the same patients in selected gliomas encompassing grade II to IV. Despite the characteristic heterogeneity of gliomas, we found substantial similarities between the corresponding aspirates and TCRs that included mutations used in the clinical routine and glioma-associated transcriptional signatures. Based on these results, we confirmed the suitability of CUSA-fixed biomaterial from glioma surgeries for downstream applications.

overall_design: Two types of comparisons: (i) between grade IV and grade II/III samples, independently of the origin of the tissue (TCR, aspirate) (n = 4 for each condition), and (ii) between TCR and CUSA-derived material, independently of the diagnosis and degree (n = 4 for each condition).


title: Single-cell ATAC-Seq of recurrent pediatric high-grade glioma

city: Calgary

first: Marco

last: Gallo

state: Alberta

address: 3330 Hospital Drive NW, Heritage Medical Research Building

department: Cumming School of Medicine

institute: University of Calgary

summary: We performed scATAC-seq on  glioblastoma tissue samples taken at time of recurrence to map the global chromatin profiles of glioblastoma cells and associated non-neoplastic cells

overall_design: scATAC-seq of  patient-derived pediatric glioblastoma tissue

first: Divya

last: Singhal

first: Ana

last: Nikolic

first: Katrina

last: Ellestad


title: ScRNAseq - Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration

city: Vienna

first: Sunanjay

last: Bajaj

address: Dr.-Bohr-Gasse 3

institute: Institute for Molecular Biotechnology of the Austrian Academy of Sciences

summary: We use cerebral organoid fusions and a novel migration tracking platform to understand the functional impact of neurotransmitter signaling on migrating human interneurons.

overall_design: Four samples with dorsal and ventral fusion at day 70 and day 90.

first: Joshua

last: Bagley

first: Christoph

last: Sommer

first: Abel

last: Vertesy

first: Veronica

last: Krenn

first: Sakurako

last: Wong

first: Julie

last: Lévi-Strauss

first: Juergen

last: Knoblich


title: Single-cell ATAC-Seq of pediatric high-grade glioma

summary: We performed scATAC-seq on  glioblastoma tissue samples taken at time of initial surgical resection to map the global chromatin profiles of glioblastoma cells and associated non-neoplastic cells

overall_design: scATAC-seq of primary patient-derived pediatric glioblastoma tissue


title: Class I histone deacetylases (HDAC) critically contribute to Ewing sarcoma pathogenesis III

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

summary: Background: Ewing sarcoma (EwS) are characterized by oncogenic chimeric EWS-ETS proteins. EZH2 is upregulated via predominant EWS-FLI1 in EwS. RNAi of EZH2 revealed an EZH2-maintained, undifferentiated, stemness phenotype. Herein, microarray analysis demonstrated that treatment with HDAC inhibitors (HDACi) entinostat or TSA resulted in the induction of a similar pattern of differentiation genes as observed after EZH2 RNAi. This indicates that EZH2-containing PRC2 complexes may serve as a building block of class I HDAC activity in EwS.  Methods: The role of class I HDACs was determined using different inhibitors including TSA, romidepsin (FK228), entinostat (MS-275) and PCI-34051 as well as CRISPR/Cas9 class I HDAC knock outs and HDAC RNAi. To analyze resulting changes microarray and gene set enrichment analysis (GSEA), qRT-PCR, western blotting, Co-IP, proliferation, apoptosis, differentiation, invasion assays and xenograft-mouse models were used.  Results: Class I HDACs are constitutively expressed in EwS. They seem regulated via EWS-FLI1. Interestingly, patients with high levels of individual class I HDAC expression show decreased overall survival. CRISPR/Cas9 class I HDAC knock out of individual HDACs such as HDAC1 and HDAC2 inhibited growth, invasiveness, and blocked local tumor growth in xenograft mice. Microarray and GSEA analysis demonstrated that treatment with individual HDAC inhibitors (HDACi) blocked an EWS-FLI1 specific expression profile, while entinostat in addition suppressed metastasis relevant genes. EwS cells demonstrated increased susceptibility to treatment with first line chemotherapeutics including doxorubicin in the presence of HDACi. Furthermore, HDACi treatment mimicked RNAi of EZH2 in EwS. Treated cells showed diminished growth capacity, but an increased endothelial as well as neuronal differentiation ability. HDACi synergizes with EED inhibitor (EEDi) in vitro and together inhibited tumor growth in xenograft mice. Co-IP experiments identified HDAC class I family members as part of a regulatory complex together with PRC2.  Conclusion: Class I HDAC proteins seem to be important mediators of the pathognomonic EWS-ETS-mediated transcription program in EwS and in combination therapy, co-treatment with HDACi are interesting new treatment opportunities for this malignant disease.

overall_design: Ewing sarcoma cell lines CHLA-10 or SK-N-MC were treated either with A-395, FK228, MS-275 or acombination of  A-395+ FK228 or A395+MS-275 or solvent control for 27 hrs at 37 °C, 5% CO2 respectively.

first: Oxana

last: Schmidt

first: Nadja

last: Nehls

first: Günther


title: Identification of Nuclear Export Inhibitor-Based Combination Therapies in Preclinical Models of Triple-Negative Breast Cancer

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: An estimated 284,000 Americans will be diagnosed with breast cancer in 2021. Of these individuals, 15-20% will be diagnosed with basal-like triple-negative breast cancer (TNBC), which is known to be highly metastatic. Chemotherapy is standard of care for TNBC patients, but acquired chemoresistance is a common clinical problem. There is currently a lack of alternative, targeted treatment strategies for TNBC; this study sought to identify novel therapeutic combinations to treat basal-like TNBCs. For these studies, a set of four human basal-like TNBC cell lines was utilized to determine the cytotoxicity profile of 1,363 unique clinically-used drugs. Ten promising therapeutic candidates were identified, and synergism studies were performed in vitro. Two drug combinations that included KPT-330, an XPO1 inhibitor, were synergistic in all four cell lines. In vivo testing of four basal-like patient-derived xenografts identified a combination, KPT-330 and GSK2126458 (a PI3K/mTOR inhibitor), that decreased tumor burden in mice significantly more than monotherapy with either single agent. Bulk and single-cell RNA-sequencing, immunohistochemical studies, and analysis of published genomic datasets found that XPO1 was abundantly expressed in human basal-like TNBC cell lines, patient-derived xenografts, and patient tumor samples; within basal-like patients, XPO1 overexpression was associated with greater rates of metastases. These studies identify a promising new combination therapy for patients with basal-like TNBC.

overall_design:
PDX, Primary Tumor from Patient Derived Xenograft (PDX), and Primary Patient Tumor (TNBC) samples were examined.
The individual samples were analyzed using CellRanger v 3.1 and the Seurat R package with number of cells ranging from 1,462 to 5,819.

first: Narmeen

last: Rashid

first: Amy

last: Olex

first: Mikhail

last: Dozmorov

first: J

middle: C

last: Harrell


title: Epigenetic profiling of cells following WM-1119 treatment

first: Jinyang

last: Li

summary: ChIP-seq analysis of MOLM-13 human leukemia cells treated with DMSO or WM-1119 for 4 days

overall_design: KAT6A promotes AML differentiation block. To test the effect of KAT6A inhibition on the epigenetic program of AML cells, we utilized a small molecule inhibitor targeting KAT6A to treat MOLM-13 human AML cells and performed ChIP-seq.

first: Fangxue

last: Yan

first: Andres

last: Blanco


title: Epigenetic profiling of cells following KAT6A CRISPR targeting

summary: ChIP-seq analysis of MOLM-13 human leukemia cells transduced with lentivirus containing CRISPR-Cas9 EV or sgKAT6A for 5 days.

overall_design: KAT6A promotes AML differentiation block. To test the effect of KAT6A inhibition on the epigenetic program of AML cells, we utilized CRISPR-Cas9 technique and delete KAT6A in MOLM-13 human AML cells and performed ChIP-seq.


title: Class I histone deacetylases (HDAC) critically contribute to Ewing sarcoma pathogenesis

summary: This SuperSeries is composed of the SubSeries listed below.


title: Class I histone deacetylases (HDAC) critically contribute to Ewing sarcoma pathogenesis I

overall_design: Ewing sarcoma cell lines A673, CHLA-10, EW7 or SK-N-MC were treated either with HDAC inhibitors FK228, MS-275, PCI-34051, TSA, or solvent control for 17 hrs at 37 °C, 5% CO2 respectively. Cell lines EW7 and SK-N-MC in addition were treated either with Doxorubicin, Vincristine or a combination of Doxorubicin or Vincristine with FK228, MS275 or PCI-34051, respectively.


title: RNAseq of old and young males with equal physical activity

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: 18 older (65-71 years) and 20 young (19-25 years) males were recruited based on similar, self-reported physical activity, which was verified using accelerometry measurements. Gene expression profiles of vastus lateralis biopsies obtained by RNA sequencing. A clear ageing signature was observed despite similar physcical activity.

overall_design: Cross-sectional

first: Bart

last: Lagerwaard

first: Arie

middle: G

last: Nieuwenhuizen

first: Vincent

last: de Boer

first: Jaap

last: Keijer


title: Endothelial Jak3 expression enhances pro-hematopoietic angiocrine function

city: New York

first: José Gabriel

last: Barcia Durán

address: 1300 York Avenue, Room A-809

institute: Weill Cornell Medicine

summary: Jak3 is the only non-promiscuous member of the Jak family of secondary messengers. Jak3–/– mice display defective T and NK cell development, which results in a SCID phenotype. As a result, studies to date have focused on understanding and targeting the cell-autonomous role of Jak3 in immunity, while functional Jak3 expression outside the hematopoietic system remains largely unreported. We show that Jak3 is expressed in endothelial cells across hematopoietic and non-hematopoietic organs, with heightened expression in the bone marrow. The bone marrow niche is understood as a network of different cell types that regulate hematopoietic function. We show that the Jak3–/– bone marrow niche is deleterious for the maintenance of long-term repopulating hematopoietic stem cells (LT-HSCs) and that JAK3-overexpressing endothelial cells have increased potential to expand LT-HSCs in vitro. Increased arterial zonation in the bone marrow of Jak3–/– mice further situates Jak3 as a marker of sinusoidal endothelium. This work may serve to identify a novel function for a highly specific tyrosine kinase in the bone marrow vascular niche and to further characterize the LT-HSC function of sinusoidal endothelium.

overall_design: Transcriptome sequencing of liver, lung, heart, kidney, and bone marrow endothelial cells.

first: José

first: Sean

last: Houghton

first: David

last: Redmond

first: Raphaël

last: Lis


title: Transcriptional profiling of cells following WM-1119 treatment

summary: RNA-seq analysis of MOLM-13 human leukemia cells or mouse ER-Hoxa9 treated with DMSO or WM-1119 for 4 days

overall_design: KAT6A promotes AML differentiation block. To test the effect of KAT6A inhibition on the transcriptional program of AML cells, we utilized a small molecule inhibitor targeting KAT6A to treat MOLM-13 human AML cells and mouse ER-Hoxa9 cells and performed RNA-seq.


title: Expression data from epidermal human skin (stem cells, transient amplifying cells, differentiated cells)

city: Amman

first: Deema

middle: Adnan

last: Ali

address: queen Rania street

department: cell therapy center

country: Jordan

institute: The University of Jordan

summary:
Performing global gene expression profiling for different types of keratinocytes colonies can provide important information that might help in understanding the biology and ontogeny of epidermal skin stem cells.
We used microarrays to detail the global  gene expression profiling for different types of keratinocytes colonies including Holoclones (stem cells), Meroclones (transient amplifying cells), and Paraclones (differentiated cells) .

overall_design: A total of 100 colonies per foreskin sample (n=6) were analyzed. The classification was based  on the percentage of aborted colonies (< 3 mm2 in diameter); When 0–5% of colonies were aborted the clone was scored as holoclone which represents the stem cells. When more than 95% of the colonies were aborted, the clone was classified as paraclone which represents the differentiated cells. When more than 5%, but less than 95% of the colonies were aborted, the clone was classified as meroclone which represent transient amplifying cells

first: Dana

last: Hattab

first: Abdalla

last: Awidi


title: ChIP-seq analysis of HA-KAT6A in MOLM-13 AML cells

summary: ChIP-seq analysis of MOLM-13 human leukemia cells with overexpression of WT KAT6A with HA tag.

overall_design: KAT6A promotes AML differentiation block. To assess where KAT6A is localized in the genome, MOLM-13 cells were overexpressed with WT KAT6A with HA tag and analyzed with ChIP-seq.


title: Class I histone deacetylases (HDAC) critically contribute to Ewing sarcoma pathogenesis II

first: Guenther

last: Richter

overall_design: Ewing sarcoma cell lines CHLA-10, EW7 or SK-N-MC were lentiviraly infected with Cas9 expression plasmids and subsequently with sgRNAs specific for HDAC1 or HDAC2, respectively.  Stable clones were generated from these infectants and cultivated at 37 °C, 5% CO2 respectively.

first: Oxana

last: Schmidt

first: Nadja

last: Nehls

first: Günther


title: Effect of nanosecond pulsed electric field (nsPEF) on gene expression in TM3 Leydig cells

city: Warsaw

first: Alicja

last: Trebinska-Stryjewska

address: gen. S. Kaliskiego 2

department: Institute of Optoelectronics

country: Poland

institute: Military University of Technology

summary: The aim of our study was to analyze cell response to nanosecond pulsed electric field (nsPEF) at the gene expression level. TM3 Leydig cells were used as a model. Transcriptomics analysis was carried out immediately after exposure (0 h) and 4 or 24 h after treatment.

overall_design: TM3 Leydig cell line was exposed to nanosecond pulsed electric field (nsPEF). The generated pulses had quasi-rectangular shape, 60 ns pulse width, and 5.5 kV amplitude, which corresponded to an electric field of 14 kV/cm. In total, 80 pulses were applied at the repetition rate of 26.4 pulses per minute. Gene expression in nsPEF-exposed or sham-exposed TM3 cells was measured immediately after (0 h), 4 and 24 h after exposure. Four biological replicates were analyzed for each time point and each condition.

first: Elzbieta

last: Trafny


title: Histone demethylase KDM6A promotes somatic cell reprogramming by epigenetically regulate PTEN and IL-6 signal pathway

city: harbin

first: Qi

last: Jiang

state: heilongjiang

address: baojian road 157

department: Department of histology and embryology

institute: Harbin Medical University

overall_design: Refer to individual Series


title: Histone demethylase KDM6A promotes somatic cell reprogramming by epigenetically regulate PTEN and IL-6 signal pathway [ChIP-seq]

summary: Aberrant epigenetic reprogramming is one of the major barriers for somatic cell reprogramming. Although our previous study has demonstrated that KDM6A, a H3K27me3 demethylase, could improve nuclear reprogramming efficiency, but its role in somatic cell reprogramming and the mechanism remain unclear. In this study, we demonstrated that overexpression of Kdm6a could improve iPSC reprogramming efficiency in a demethylase enzymatic activity-dependent manner. And Kdm6a overexpression changed the gene expression profile and metabolic pattern through erasing the repressive H3K27me3 in fibroblast. Besides, we proved that KDM6A could promote IL-6 expression in MEF cells and the secreted IL-6 also could improve iPSC reprogramming efficiency. Furthermore, we found that KDM6A could promote PTEN expression, further regulate p-AKT and p-mTOR levels, which favor the reprogramming, and interference of PTEN could counteracted the promotion effect of KDM6A. Taken together, our data revealed that KDM6A could promote iPSC reprogramming efficiency by accelerate the change of gene expression profile and metabolic pattern in a demethylation-activity-dependent manner, which may give insight to the relationship between epigenetic modification and somatic cell reprogramming.

overall_design: Examination of H3K27me3 in MEFs after infection of KDM6A or CON vector.

first: Lei

last: Lei


title: Transcriptional profiling of MOLM-13 AML cells following KAT6A CRISPR targeting

first: Jinyang

last: Li

summary: RNA-seq analysis of MOLM-13 human leukemia cells transduced with lentivirus containing CRISPR-Cas9 EV or sgKAT6A for 5 days

overall_design: KAT6A promotes AML differentiation block. To test the effect of KAT6A inhibition on the transcriptional program of AML cells, we utilized CRISPR-Cas9 technique and delete KAT6A in MOLM-13 human AML cells and performed RNA-seq.

first: Fangxue

last: Yan

first: Andres

last: Blanco


title: Histone demethylase KDM6A promotes somatic cell reprogramming by epigenetically regulate PTEN and IL-6 signal pathway [RNA-seq]

overall_design: 48 hrs after infection or 72h post DOX was added, the total RNA of 4F2A MEFs was harvested by using TRIzol reagent (Invitrogen), each group was prepared with three parallel replicates. Then, all the samples were sent to BGI Corporation (China) for further RNA-seq analysis via BGISEQ-500 sequencer. The GO and KEGG pathway analyses were performed based on the KEGG database on the Dr. Tom network platform of BGI (http://report.bgi.com).


title: Identification of a T cell lymphoma in plkcGAPDH transgenic mice

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

type: Genome variation profiling by high throughput sequencing


title: Identification of a T-cell lymphoma in plkcGAPDH transgenic mice (Exome)

summary: Glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) is emerging as a key player in T-cell development, function and cancer. Here we investigated the role of GAPDH in T-cell development/function by overexpressing GAPDH in the T-cell lineage. Aged mice developed: 1) splenomegaly, 2) enlarged lymph nodes, 3) lymphocyte-infiltrations in the liver and bone marrow. All showed an increase of strongly proliferating and clonal Tfh CXCR5+PD1highCD4+-T cells associated with germinal center B cells and inflammatory cytokine-release. Gene-set-expression-analysis confirmed that this lymphoma was equivalent to human angioimmunoblastic T-cell lymphoma (AITL). Mechanistically, GAPDH induced NF-kB pathway in the murine AITL in vivo inhibition of NF-kB combined with anti-PD1 increased mice survival and cancer immune response. GAPDH-dependent modulation of NF-kB in T-cells allowed to model AITL-disease and evaluate treatments.

overall_design: Whole exome sequencing of CD4+ T-cells isolated from plkcGAPDH transgenic mice

first: E

last: Verhoeyen

first: R

last: Mhaidly

first: Celia

last: Shuran


title: NanoString Human PC3 nCounter PanCancer IO 360 panel

status: Public on Oct 19 2021

city: Gaithersburg

first: Ezra

middle: Myung Chul

last: Chung

state: MD

address: 401 Professional Dr. Suite 250

department: R&D

institute: STCube Pharmaceuticals

summary: The goal of this study was to investigate the roles of Butyrophilin Subfamily 1 Member A1 (BTN1A1) in terms of the signaling pathway after overexpression of BTN1A1A1 gene. To this end, we conducted NanoString analysis. From NanoString analysis with BTN1A1-overexpressing PC3 cells, we concluded that BTN1A1 play a pivotal role in the regulation of several signaling pathway including Jak-STAT pathway that is involved in processes such as immunity, cell division, cell death and tumor formation.

overall_design: PC3 cells and BTN1A1-overexpressing PC# cells were treated Interferon-gamma (100 ng/ml) for 24 and 48 hours, total RNAs were extracted using a combination of Trizol and a commercial kit (Qiagen Rneasy mini kit). The RNAs were applied to the PanCancer IO 360 panel (NanoString Technologies, Inc.).

first: Stephen

last: Yoo


title: Pancreatic Tumor Microenvironment Maintains Tumor Growth through Nucleosides Secretion

city: 北京

first: YU

last: ZHANG

state: non-US Resident

address: XUEYUANLU No.38 Haidian District, PKUHSC Anatomy Building

institute: Peking Univ.

summary: Cancer-associated fibroblasts (CAFs) are one of the most prominent and active components in the pancreatic tumor microenvironment. Our data show that CAFs are critical for PDAC survival upon glutamine deprivation. Specifically, we uncovered a role for nucleosides, which are secreted by CAFs through autophagy in an NUFIP1-depenent manner, increased glucose utilization and promoted growth of PDAC. Moreover, we demonstrate that CAF-derived nucleosides induced glucose consumption under glutamine-deprived conditions and displayed a dependence on MYC. Using an orthotopic mouse model of PDAC, we found that inhibiting nucleoside secretion by targeting NUFIP1 in the stroma reduced tumor weight. This finding highlights a previously unappreciated metabolic network within pancreatic tumors in which diverse nutrients are used to promote growth in an austere tumor microenvironment.

overall_design: 2 samples.14837 PDAC cells were treated with CAF conditional medium or 14837 conditional medium. Cells' RNA was harvested using Trizol reagent. 2 ug of total RNA is used for the construction of sequencing libraries by Novaseq 6000.

first: Meng

last: Yuan

first: Ying

last: Zhao


title: RNAseq of Jurkat_control and Jurkat_shPPM1A-AS

city: Tianjin

first: Guoli

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: To study the effect of PPM1A-AS on T-cell acute lymphoblastic leukemia (T-ALL) cells, we conducted shRNA-mediated knockdown of PPM1A-AS in Jurkat and performed RNA-seq.

overall_design: mRNA profiles of control and PPM1A-AS knockdown Jurkat

first: Zhe

last: Liu

first: Kegan

last: Zhu


title: Identification of a T cell lymphoma in plkcGAPDH transgénic mice (RNA-Seq)

summary: Glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) is emerging as a key player in T-cell development, function and cancer. Here we investigated the role of GAPDH in T-cell development/function by overexpressing GAPDH in the T-cell lineage. Aged mice developed: 1) splenomegaly, 2) enlarged lymph nodes, 3) lymphocyte-infiltrations in the liver and bone marrow. All showed an increase of strongly proliferating and clonal Tfh CXCR5+PD1highCD4+-T cells associated with germinal center B cells and inflammatory cytokine-release. Gene-set-expression-analysis confirmed that this lymphoma was equivalent to human angioimmunoblastic T-cell lymphoma (AITL). Mechanistically, GAPDH induced NF-B pathway in the murine AITL in vivo inhibition of NF-B combined with anti-PD1 increased mice survival and cancer immune response. GAPDH-dependent modulation of NF-B in T-cells allowed to model AITL-disease and evaluate treatments.

overall_design: mRNA profiles of lymphomas from plckGAPDH mice  were generated by RNA sequencing (RNASeq), in triplicate, using Illumina GAIIx.

first: A

last: Paquet

first: N

last: Pons

first: K

first: P

last: Barbry

first: M

last: Tosolini


title: Fusobacterium nucleatum promotes colorectal cancer metastasis through miR-1322/CCL20 axis and M2 polarization

city: Zhejiang

first: chaochao

last: xu

state: State...

address: Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, China

institute: zhejiang University

summary: Fusobacterium nucleatum-treated LoVo cells reported an increased promoting CRC metastasis effect compared with PBS control. To understand the underlying mechanisms of Fusobacterium nucleatum-induced metastasis ability of CRC cells, we performed RNA-sequencing in LoVo cells s with or without Fusobacterium nucleatum treatment with three independent biological replicates.

overall_design: Examination of  gene expression variation in LoVo cells treated with or without Fusobacterium nucleatum (MOI of 100:1)

first: Chaochao

last: Xu

first: Shujie

last: Chen


title: Expression profiles of epicardial and subcutaneous adipose tissue

city: Paris

first: Corneliu

last: Henegar

state: Ile de France

address: 15 Rue de l'Ecole de Medecine

institute: Institut national de la santé et de la recherche médicale

summary:
The epicardial adipose tissue (EAT) is a visceral adipose tissue in close contact with coronary vessels whose increase is associated with coronary artery disease (CAD). Our goal was to identify candidate molecule(s) characterizing EAT which could intervene in the pathogenesis of CAD. An approach combining microarrays and bioinformatic sequence analysis tools for predicting secreted proteins (TargetP) was applied to paired biopsies of subcutaneous adipose tissue (SAT) and EAT, obtained from patients with or without CAD (NCAD). Results were validated in 3 independent groups of subjects by RT-qPCR, western blot, immuno histochemistry and explants secretion. sPLA2-IIA ranked first among genes coding for potentially secreted proteins with the highest overexpression in EAT in both CAD and NCAD. RT-qPCR confirmed its increased expression in EAT ( p<0.01) and in EAT from CAD as compared to NCAD (49.3 ±13 vs. 17.4 ± 9.7  p<0.01). sPLA2-IIA protein level was higher in EAT than in SAT. EAT explants demonstrated also significantly higher sPLA2-IIA secretion levels than SAT ones (4.37±2.7 vs 0.67± 0.28 ng.ml-1/g tissue/24h,p<0.03). sPLA2-IIA labeling was evidenced in EAT in the stroma vascular fraction between adipocytes and in connective capsules, with no immunostaining of the adipocytes. SAT was weakly labeled following the same pattern.
Conclusion: We evidenced for the first time an increased expression of sPLA2-IIA in EAT from patients with CAD, a phospholipase that was shown to be an independent risk factor for CAD. These findings suggest a potentially pathophysiological role of EAT in CAD.

overall_design: We studied three independent groups of subjects. Group 1 and 2 were composed of 30 subjects who underwent cardiac surgery for coronary artery disease (CAD) or for valve replacement, or myxoma resection (NCAD). Patients from the NCAD group had no clinical or angiographic sign of CAD, and had a left ventricular ejection fraction > 50%. Group 3 was composed of 15 non diabetic patients with CAD. EAT and SAT samples were obtained within 20 min after the start of surgery respectively near the proximal tract of the right coronary artery and the site of chest incision. Samples were frozen in liquid nitrogen and stored at -80 °C. In groups 1 and 2, total RNA obtained from SAT and EAT samples of 7 subjects (4 CAD and 3 NCAD) was prepared using the RNeasy total RNA Mini kit (Qiagen). RNA concentration and integrity were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France). For microarray experiments, 1 µg of total RNA from each total RNA sample preparation was amplified by MessageAmp RNA Kit (Ambion, Austin, TX, USA) and 3 µg of amplified RNA was labeled with cyanin dyes (Cy) using the CyScribe First-Strand cDNA labeling kit (Amersham Biosciences, Orsay, France). (available at http://cmgm.stanford.edu/pbrown/protocols/index). Using pangenomic Agilent® cDNA microarrays, we compared the expression profiles of EAT and SAT from CAD and NCAD subjects. To this purpose we used a common reference pool that was generated by mixing equal amounts of total RNA extracted from adipose tissue samples of patients undergoing plastic surgery. Amplified RNA (aRNA) from the reference pool was labeled with Cy3, and aRNA from the 7 subjects (either EAT or SAT) was labeled with Cy5. A total of 13 pangenomic microarray hybridizations were performed for this differential comparison. After scanning the 13 arrays, the images were analyzed and data were normalized using the Stanford Microarray Database Online resources (http://genomewww5.stanford.edu/MicroArray/SMD/).

first: Karine

last: Clement

first: Veronique

last: Pelloux

first: Anne

last: Dutour

first: Vincent

last: Achard

first: Alina

last: Silaghi

first: Flavien

last: Jacques


title: Yap Promotes Outbound Noncanonical Wnt Signaling from Cardiomyocytes to Fibroblast to Enhance Neonatal Heart Regeneration

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We used Bulk RNA sequencing to determine the global transcriptional effects of Wls cKO in cardiomyocytes on mouse injury response after MI.

overall_design: Cardiomyocytes and Non-Cardiomyocytes were collected from each mice. Each mice received three consecutive doses of TAM from P1-P3, and mice underwent MI at P2. Samples were collected 2 weeks are surgery. 3 Hearts were collected from each experimental condition.

first: Shijie

first: Tang

last: Li

first: James

middle: F

last: Martin


title: Identification of enhancer-promoter contacts in squamous cancer cells [HiChIP]

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

summary: Profiling promoter-enhancer interactions in squamous cancer cell lines

overall_design: HiChIP of H3K27ac in squamous cancer cell lines

first: Yanli

last: Liu


title: Metabolic skewing in inflammatory hepatic Th17 cells regulates non-alcoholic fatty liver disease (NAFLD) pathogenesis

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary:
Purpose: To determine the Th17 milleu in the liver during NAFLD in the context of Diet induce obesity
Methods: Mice were place on a highfat diet for 20 weeks, Th17 cells were isolated from the liver by FACS sorting the TCRb+CD4+IL-17A-GFP+ cells. Single cells were separated into 6 C1 capture chips and RNA sequencing was performed at an average depth of 3 million paired-end reads (75nt) using the Illumina HiSeq 2500, with SMART-Seq2 version 2 chemistry as recommended by the manufacturer.
Results: Here, we demonstrate that NAFLD progression is associated with polarization and accumulation of a unique population of inflammatory hepatic CXCR3+Th17 cells (ihTh17) in mice. Transfer of ihTh17 cells accelerated and exacerbated NAFLD pathogenesis in vivo. Notably, ihTh17 cells, compared to conventional CXCR3-Th17 cells, exhibited increased open chromatin marks in enhancer regions, increased metabolic capacity, and were able to simultaneously produce an array of proinflammatory cytokines which directly contributed to hepatocellular damage. Modulation of the CXCR3-CXCL9/10 axis and ihTh17 metabolic state was sufficient to reverse ihTh17-centric inflammatory vigor and NAFLD severity.
Conclusions:  In sum, our data show that the obesity-associated environment regulates Th17 cell competence towards an ihTh17 fate and that the preferential use of glycolytic pathways in ihTh17 cells promotes their inflammatory vigor and contributes to NAFLD progression.

overall_design: Single cell mRNA profiles of Th17 cell form the liver of Diet induce obesity mice were generated

first: Maria

last: Moreno-Fernandez

first: Daniel

last: Giles

first: Jarren

middle: R

last: Oates

first: Calvin

last: Chan

first: Michelle

middle: S

last: Damen

first: Jessica

last: Doll

first: Traci

last: Stankiewicz

first: Xiaoting

first: Chetal

last: Kashish

first: Rebekah

last: Karns

first: Matthew

last: Weirauch

first: Lindsey

last: Romick-Rosendale

first: Stavra

last: Xanthakos

first: Rachel

last: Sheridan

first: Sara

last: Szabo

first: Amy

last: Shah

first: Michael

last: Helmrath

first: Thomas

last: Inge

first: Hitesh

last: Deshmukh

first: Senad

last: Divanovic


title: Identification of enhancer-promoter contacts in squamous cancer cells [ChIP-seq]

first: Xiaoyang

last: Zhang

summary: Profiling the histone modification H3K27ac, the co-activator BRD4 and the transcription factor SOX2 in squamous cancer cell lines

overall_design: Chromatin Immunoprecipitation-sequencing (ChIP-seq) of H3K27ac, BRD4 and SOX2 in squamous cancer cell lines

first: Yanli

last: Liu


title: Identification of enhancer-promoter contacts in squamous cancer cells [RNA-seq]

summary: Gene expression profiling in squamous cancer cells under different genetic or chemical perturbations

overall_design: RNA-seq in squamous cancer cells under different genetic or chemical perturbations


title: Membrane Peptolytic Signals on a Fibroblast Subset Dictate Cancer Stem Cell Fate by Regulating Lipid Metabolism

city: Guangzhou

first: shubin

last: Yu

address: YANJIANG XILU

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: Carcinoma-associated fibroblasts (CAFs) consist of heterogeneous subpopulations and play a critical role in the dynamics of the tumor microenvironment. Previously, the extracellular signals of CAFs have been attributed to extracellular matrix, cytokine, cell-surface checkpoints and exosome. Here, we showed that CD10, which is a transmembrane hydrolase expressed on a subset of CAFs, supports tumor stemness and induced chemoresistance. Mechanistically, CD10 degenerates an anti-tumoral peptide, osteogenic growth peptide (OGP). OGP restrains the expression of a rate-limiting desaturase and inhibits lipid desaturation which is required for cancer stem cells (CSCs). Therapeutically, targeting CD10 significantly improves the efficacy of chemotherapy in vivo. Clinically, CD10-OGP signals are associated with the response of neo-adjuvant chemotherapy in patients of breast cancer. Overall, our data suggested that a nexus between the niche and lipid metabolism in CSCs can be a promising therapeutic target for breast cancer.

overall_design: Transcriptome profile of MCF-7mammo treated with or without osteogenic growth peptide (OGP)  were generated by deep sequencing using Illumina Novaseq™ 6000.

first: Shubin

first: Yiwen

last: Lu


title: Sequencing of Mus musculus skin of two different age groups

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary: Comparison of gene expression profiles from Mus musculus skin of two age groups. The RNA-seq data comprise 2 groups at ages: 2 and 9 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 10 samples in 2 groups: 2 months (5 samples), 24 months (5 samples)

first: Christiane

last: Frahm

first: Otto

last: Witte

first: Madlen

last: Günther

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Intranasal administration of OM-85, a bacterial lysate, alters lung transcriptional profiles and protects against experimental asthma

city: Tucson

first: Donata

last: Vercelli

state: Arizona

address: 1657 E. Helen St.

institute: University of Arizona

summary:
Background: Microbial interventions against allergic asthma have robust epidemiologic underpinnings and the potential to recalibrate disease-inducing immune responses. Oral administration of OM-85, a standardized lysate of human airways bacteria, is widely used empirically to prevent respiratory infections, and a clinical trial is testing its ability to prevent asthma in at-risk children. On the other hand, we previously showed that intra-nasal administration of products from microbe-rich farm environments abrogate experimental allergic asthma.
Objectives: To investigate whether direct administration of OM-85 to the airway compartment protects against experimental allergic asthma, and to identify protective cellular and molecular mechanisms activated through this natural route.
Methods: BALB/cJ mice (7-8 weeks old) sensitized and challenged with Ovalbumin received OM-85 intra-nasally, and cardinal cellular and molecular asthma phenotypes were measured. Murine lung gene expression was profiled by RNA-sequencing.
Results: Airway administration of OM-85 suppressed allergic asthma and altered the transcriptome profile in unfractionated lung tissue.
Conclusion We provide the first demonstration that administration of a standardized bacterial lysate to the airway compartment protects from experimental allergic asthma by engaging multiple immune pathways.

overall_design: Transcriptome profiling in unfractionated lung tissue from mice treated intranasally with bacterial lysate (OM-85)

first: Vadim

last: Pivniouk

first: Avery

last: DeVries


title: The gene expression profile of humanized rat livers

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: We investigated the transcriptome of repopualted human hepatocytes in humanized rat livers.

overall_design: Human hepatocytes were transplanted to the livers of Fah-/-Rag2-/-IL2rg-/- rat. After liver xeno-repopulation, RNA extracted from the whole-liver homogenates of humanzied rat livers was used for RNA-sequencing.

first: Ludi

first: Jian-Yun

last: Ge

first: Baihua

last: Wu

first: Yun-Wen

last: Zheng


title: Epigenome analysis of normal and FHRCC samples

city: Chengdu

first: Guangxi

last: Sun

address: No.37 Guoxue Alley, Wuhou District, Chengdu City, Sichuan Province, PR China

institute: West China hospital, sichuang university

summary: Genome wide DNA methylation profiling of 32 hereditary leiomyomatosis and renal cell cancer patient-derived samples. The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in nine breast HMECs samples.

overall_design: Bisulphite converted DNA from the 32 samples (normal and FHRCC) were hybridized to the Illumina Infinium 850k Human Methylation Beadchip

first: Hao

last: Zeng


title: RNA-seq of young and quiescent (9 days) MRC-5 human fibroblasts

first: JenAge

summary: Comparison of gene expression profiles of quiescent MRC-5 fibroblasts and young MRC-5 fibroblasts.    Jena Centre for Systems Biology of Ageing – JenAge (www.jenage.de)

overall_design: 6 samples in 2 groups: quiescent MRC-5 fibroblasts (3 samples), young MRC-5 fibroblasts (3 samples)

first: Shiva

last: Marthandan

first: K

last: Klement

first: Steffen

last: Priebe

first: Stephan

last: Diekmann

first: Peter

last: Hemmerich


title: Next Generation Sequencing (NGC) Analysis of Gene Expression Proliles in Human Gingiva-derived Mesenchymal Stem Cells (GMSCs) Cultured in Methacrylated 3D-Collagen Hydrogel Compared to 2D-cultured Counterparts

city: Philadelphia

first: Qunzhou

last: Zhang

state: PA

address: Levy Building 545, 240 S 40th Street, Philadelphia

institute: University of Pennsylvania School of Dental Medicine

summary:
Purpose: The goals of this study are to perform NGC analysis in order to compare the gene expression profiles of GMSCs cultured in 3D-collagen hydrogel and their 2D-cultured counterparts.
Methods:  mRNA profiles of 3D- and 2D-cultured GMSCs were generated by deep sequencing, in triplicate, using Illumina Xten. The read alignment is done using HISAT2 v.2.0.5 software with Ensembl GRCh38 genome as reference genome. Transcripts Assembly  is done using StringTie v.1.3.3b software. Significant DE genes or transcripts (q-value < 0.05) were extracted by edgeR (R package) for each comparison groups. DEGs were analyzed with gene ontology enrichment analysis and KEGG by R software with clusterProfiler package. Significant GO or KEGG terms (FDR-value < 0.05) were extracted using hypergeometric distribution. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, significant differentially expressed genes (DEGs) were defined as those with a log2 fold change (FC) ≥1 (GMSC-3D v.s.GMSC-2D) and a false discovery rate (FDR) of ≤ 1%. A total of 5588 DEGs, including 3476 upregulated and 2112 downregulated genes were identified between 3D-cultured GMSCs and 2D-cultured counterparts with a fold change ≥1.0 and p value <0.05.  Altered expression of 17 genes reltaed to neural crest stem cells, mesenchymal cells, and NOTCh signaling pathways was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical cluster analysis revealed a different hierarchical clustering algorithm between 3D- and 2D-cultured GMSCs as illustrated in the Heatmap, which uncovered several as yet uncharacterized clusters of genes that may contribute to the conversion of GMSCs into neural crest stem-like (NCSC) or Schwann cell precursor (SCP)-like cells under a defined 3D-collagen hydrogel condition.
Conclusions: Our study represents the first detailed comparative analysis of gene expression profiles between 2D- and 3D-cultured GMSCs, with biologic replicates, generated by RNA-seq technology. Our RNA-seq results show that GMSCs cultured in defined 3D-collagen hydrogel underwent conversion into neural crest stem-like (NCSC)/Schwann cell precursor-like (SCP) cells charcaterized by upregulation of a panel of neural crest-related genes, NOTCH signaling components, and downregulation of a panel of mesenchymal cell-related genes. We conclude that RNA-seq based transcriptome characterization would permit further dissection of complex molecular mechanisms underlying 3D collagen hydrogel-driven conversion of GMSCs into NCSC/SCP-like cells..

overall_design: mRNA profiles of GMSCs cultured under regular 2D- and defined 3D-culture conditions

first: Anh

middle: D

last: Le


title: Sequencing of Nothobranchius furzeri skin in 39 weeks old animals

last: Project

type: Non-coding RNA profiling by high throughput sequencing

summary: small RNA gene expression profiles from Nothobranchius furzeri skin of 39 weeks old animals. The RNA-seq data comprise 1 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 3 samples obtained from 39 weeks old animals

first: Mario

last: Baumgart

first: Alessandro

last: Cellerino

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Sequencing of human Wi38 fibroblasts at two population doublings

summary: Gene expression profiles of human fibroblasts at different population doublings were compared. RNA-seq data comprise 2 groups: 37 and 59 population doublings.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 4 samples 2 in groups: 37 PDs (2 Samples), 59 PDs (2 Samples)

first: Rolf

last: Hühne


title: RNA-seq of NIH 3T3 and HepG2 cells after arsenite treatment

summary: Expression profiling of HepG2 human liver carcinoma cells and NIH 3T3 mouse fibroblasts after arsite treatment for 24h. RNA-seq data comprise 4 groups: NIH 3T3 mouse fibroblasts control and arsite treatment, and HepG2 human liver carcinoma cells control and arsenite treatment.       Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 8 samples in 4 groups: NIH 3T3 control (2 samples), NIH 3T3 arsite (2 samples), HepG2 control (2 samples), HepG2 arsite (2 Samples)


title: Sequencing of Danio rerio skin for 5 age groups

summary: Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA-seq data comprise 5 age groups at 6, 12, 24, 36 and 42 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 25 samples in 5 groups: 6 month (5 samples), 12 months (5 samples), 24 months (5 samples), 36 months (5 samples), 42 months (5 samples).

first: Nils

last: Hartmann

first: Christoph

last: Englert


title: Sequencing of human MRC-5 fibroblasts during replicative senescence (smallRNA)

summary: Comparison of small RNA gene expression profiles of human fibroblasts at different population doublings. RNA-seq data comprise 5 groups: 32, 42, 52, 62 and 72 Pds.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 15 samples in 5 groups: 32 PDs (3 Samples), 42 PDs (3 Samples), 52 PDs (3 Samples), 62 PDs (3 Samples), 72 PDs (3 Samples)